Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, III

Maximum Likelihood Estimation of Fitness Components in Experimental Evolution

Estimating fitness differences between allelic variants is a central goal of experimental evolution. Current methods for inferring such differences from allele frequency time series typically assume that the effects of selection can be described by a fixed selection coefficient. However, fitness is an aggregate of several components including mating success, fecundity, and viability. Distinguishing between these components could be critical in many scenarios. Here, we develop a flexible maximum likelihood framework that can disentangle different components of fitness from genotype frequency data, and estimate them individually in males and females. As a proof-of-principle, we apply our method to experimentally evolved cage populations of Drosophila melanogaster, in which we tracked the relative frequencies of a loss-of-function and wild-type allele of yellow This X-linked gene produces a recessive yellow phenotype when disrupted and is involved in male courtship ability. We find that the fitness costs of the yellow phenotype take the form of substantially reduced mating preference of wild-type females for yellow males, together with a modest reduction in the viability of yellow males and females. Our framework should be generally applicable to situations where it is important to quantify fitness components of specific genetic variants, including quantitative characterization of the population dynamics of CRISPR gene drives.

TWO NEUTRALITY TESTS OF Y-LINKED RDNA VARIATION IN DROSOPHILA MELANOGASTER

The evolutionary significance of Y-chromosomal ribosomal DNA sequence variation was tested by two different means. A single sample of males and females was collected from a peach orchard in central Pennsylvania. Wild-caught males and sons of wild-caught, wild-inseminated females were crossed to virgin females having an X-linked rDNA deficiency. Genomic DNA from male progeny of these crosses was extracted and digested with the single restriction endonuclease, DraI. Southern blots of these digestions, when probed with the complete rDNA probe, revealed 10 distinct patterns of restriction fragments. A chisquare test for the homogeneity of the frequency distributions of the sample of wild males and sons of wild females failed to reject a neutral null hypothesis. The allele frequency configuration was tested with the Ewens-Watterson test, and the departure from the infinite alleles neutral model was not significant. Simulations were performed to test the sensitivity of the tests to misclassification and to quantify the power of the two tests.

Differential fertility as a major mode of selection

Population genetic models have focused Primarily on the differential survival of genotypes as the vehicle through which selection can lead to evolutionary change. A growing body of diverse evidence suggests that differential fertility is an equally important mode of selective action. Laboratory studies with Drosophila and field studies in natural populations of plants and animals have provided direct demonstrations. Experimental ecology and reproductive biology have offered indirect but compelling evidence for the importance of differential fertility. Selection through differential fertility is not always interchangeable with selection through differential survival: the genetic dynamics can be far more complicated and can lead to unpredictable results when driven by fertility differences. The study of fertility selection in natural populations poses several problems: selection differentials can be difficult to estimate; they are likely to be very sensitive to changes in environmental conditions, and when generations overlap the fertility differential cannot be estimated correctly without demographic data. Describing the role of differential fertility in natural populations represents an emerging challenge for theoreticians and empiricists alike.